dbSNP rs1290586719: MLLT10:p.Gly365Glu (chr10-21673392-G-A) – ACMG Classification: Uncertain_significance (1 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2BP4

The NM_001195626.3(MLLT10):c.1094G>A(p.Gly365Glu) variant causes a missense change. The variant allele was found at a frequency of 0.00000224 in 1,340,504 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G365V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 30)

Exomes 𝑓: 0.0000022 ( 0 hom. )

Consequence

MLLT10
NM_001195626.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 6.03

Publications

1 publications found

Variant links:

Genes affected

MLLT10 (HGNC:16063): (MLLT10 histone lysine methyltransferase DOT1L cofactor) This gene encodes a transcription factor and has been identified as a partner gene involved in several chromosomal rearrangements resulting in various leukemias. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2010]

MLLT10 links:

ENSG00000304565 (HGNC:):

ENSG00000304565 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.31262162).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLLT10	NM_001195626.3 link	c.1094G>A	p.Gly365Glu	missense_variant	Exon 11 of 23	ENST00000307729.12	NP_001182555.1	P55197-4Q59EQ6Q6N002
MLLT10	NM_004641.4 link	c.1094G>A	p.Gly365Glu	missense_variant	Exon 11 of 24		NP_004632.1	P55197-1Q59EQ6Q6N002
MLLT10	NM_001324297.2 link	c.359G>A	p.Gly120Glu	missense_variant	Exon 13 of 25		NP_001311226.1
MLLT10	NR_136736.2 link	n.1561G>A		non_coding_transcript_exon_variant	Exon 12 of 26

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLLT10	ENST00000307729.12 link	c.1094G>A	p.Gly365Glu	missense_variant	Exon 11 of 23	1	NM_001195626.3	ENSP00000307411.7		P55197-4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00

AC:

AN:

234954

AF XY:

0.00

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000224

AC:

AN:

1340504

Hom.:

Cov.:

AF XY:

0.00000451

AC XY:

AN XY:

665266

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

29234

American (AMR)

AF:

0.00

AC:

AN:

36648

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

20906

East Asian (EAS)

AF:

0.00

AC:

AN:

30954

South Asian (SAS)

AF:

0.0000370

AC:

AN:

81096

European-Finnish (FIN)

AF:

0.00

AC:

AN:

46658

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5092

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

1037552

Other (OTH)

AF:

0.00

AC:

AN:

52364

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.608

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Uncertain

0.52

BayesDel_addAF

Uncertain

0.068

BayesDel_noAF

Benign

-0.14

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

DEOGEN2

Benign

0.14

T;.;T;T

Eigen

Uncertain

0.63

Eigen_PC

Pathogenic

0.69

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Uncertain

0.94

.;D;.;D

M_CAP

Benign

0.012

MetaRNN

Benign

0.31

T;T;T;T

MetaSVM

Benign

-1.2

MutationAssessor

Uncertain

2.0

M;M;M;M

PhyloP100

6.0

PrimateAI

Uncertain

0.74

PROVEAN

Benign

-2.1

.;N;N;N

REVEL

Benign

0.21

Sift

Uncertain

0.0070

.;D;D;D

Sift4G

Benign

0.62

T;T;T;T

Polyphen

0.97

D;.;D;D

Vest4

0.55

MutPred

0.18

Loss of glycosylation at S364 (P = 0.0388);Loss of glycosylation at S364 (P = 0.0388);Loss of glycosylation at S364 (P = 0.0388);Loss of glycosylation at S364 (P = 0.0388);

MVP

0.32

MPC

0.38

ClinPred

0.69

GERP RS

6.1

PromoterAI

-0.0062

Neutral

(source)

Varity_R

0.14

gMVP

0.23

Mutation Taster

=69/31

polymorphism

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.070

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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rs1290586719

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over